Merge branch 'Project-MONAI:dev' into 7499-torchio-transforms-wrapper

Project-MONAI · Nov 13, 2024 · 472c747 · 472c747
2 parents b896604 + 941e739
commit 472c747
Show file tree

Hide file tree

Showing 412 changed files with 30,806 additions and 2,618 deletions.
diff --git a/.github/workflows/blossom-ci.yml b/.github/workflows/blossom-ci.yml
@@ -29,13 +29,14 @@ jobs:
       args: ${{ env.args }}
 
     # This job only runs for pull request comments
-    if: contains('\
-      Nic-Ma,\
-      wyli,\
-      pxLi,\
-      YanxuanLiu,\
-      KumoLiu,\
-      ', format('{0},', github.actor)) && github.event.comment.body == '/build'
+    if: |
+      github.event.comment.body == '/build' &&
+      (
+        github.actor == 'Nic-Ma' ||
+        github.actor == 'wyli' ||
+        github.actor == 'wendell-hom' ||
+        github.actor == 'KumoLiu'
+      )
     steps:
       - name: Check if comment is issued by authorized person
         run: blossom-ci

diff --git a/.github/workflows/conda.yml b/.github/workflows/conda.yml
@@ -32,6 +32,10 @@ jobs:
         maximum-size: 16GB
         disk-root: "D:"
     - uses: actions/checkout@v4
+    - name: Clean up disk space
+      run: |
+        find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
+        rm -rf /usr/share/dotnet/
     - uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
@@ -56,6 +60,10 @@ jobs:
         conda deactivate
     - name: Test env (CPU ${{ runner.os }})
       shell: bash -el {0}
+      env:
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
       run: |
         conda activate monai
         $(pwd)/runtests.sh --build --unittests

diff --git a/.github/workflows/cron-ngc-bundle.yml b/.github/workflows/cron-ngc-bundle.yml
@@ -18,10 +18,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: cache weekly timestamp
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
@@ -13,24 +13,28 @@ jobs:
     strategy:
       matrix:
         environment:
-          - "PT191+CUDA113"
           - "PT110+CUDA113"
-          - "PT113+CUDA113"
-          - "PTLATEST+CUDA121"
+          - "PT113+CUDA118"
+          - "PT210+CUDA121"
+          - "PT240+CUDA126"
+          - "PTLATEST+CUDA126"
         include:
           # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
-          - environment: PT191+CUDA113
-            pytorch: "torch==1.9.1 torchvision==0.10.1 --extra-index-url https://download.pytorch.org/whl/cu113"
-            base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
           - environment: PT110+CUDA113
             pytorch: "torch==1.10.2 torchvision==0.11.3 --extra-index-url https://download.pytorch.org/whl/cu113"
             base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
-          - environment: PT113+CUDA113
-            pytorch: "torch==1.13.1 torchvision==0.14.1 --extra-index-url https://download.pytorch.org/whl/cu113"
-            base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
-          - environment: PTLATEST+CUDA121
-            pytorch: "-U torch torchvision --extra-index-url https://download.pytorch.org/whl/cu118"
-            base: "nvcr.io/nvidia/pytorch:23.08-py3"  # CUDA 12.2
+          - environment: PT113+CUDA118
+            pytorch: "torch==1.13.1 torchvision==0.14.1 --extra-index-url https://download.pytorch.org/whl/cu121"
+            base: "nvcr.io/nvidia/pytorch:22.10-py3"  # CUDA 11.8
+          - environment: PT210+CUDA121
+            pytorch: "pytorch==2.1.0 torchvision==0.16.0 --extra-index-url https://download.pytorch.org/whl/cu121"
+            base: "nvcr.io/nvidia/pytorch:23.08-py3"  # CUDA 12.1
+          - environment: PT240+CUDA126
+            pytorch: "pytorch==2.4.0 torchvision==0.19.0 --extra-index-url https://download.pytorch.org/whl/cu121"
+            base: "nvcr.io/nvidia/pytorch:24.08-py3"  # CUDA 12.6
+          - environment: PTLATEST+CUDA126
+            pytorch: "-U torch torchvision --extra-index-url https://download.pytorch.org/whl/cu121"
+            base: "nvcr.io/nvidia/pytorch:24.10-py3"  # CUDA 12.6
     container:
       image: ${{ matrix.base }}
       options: "--gpus all"
@@ -50,6 +54,10 @@ jobs:
         python -m pip install -r requirements-dev.txt
         python -m pip list
     - name: Run tests report coverage
+      env:
+          NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+          NGC_ORG: ${{ secrets.NGC_ORG }}
+          NGC_TEAM: ${{ secrets.NGC_TEAM }}
       run: |
         export LAUNCH_DELAY=$[ $RANDOM % 16 * 60 ]
         echo "Sleep $LAUNCH_DELAY"
@@ -76,7 +84,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:22.10", "pytorch:23.08"]
+        container: ["pytorch:23.08", "pytorch:24.08", "pytorch:24.10"]
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -94,6 +102,10 @@ jobs:
         python -m pip install -r requirements-dev.txt
         python -m pip list
     - name: Run tests report coverage
+      env:
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
       run: |
         export LAUNCH_DELAY=$[ $RANDOM % 16 * 60 ]
         echo "Sleep $LAUNCH_DELAY"
@@ -121,7 +133,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:23.08"]
+        container: ["pytorch:24.10"]
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -196,6 +208,10 @@ jobs:
     - name: Run tests report coverage
       # The docker image process has done the compilation.
       # BUILD_MONAI=1 is necessary for triggering the USE_COMPILED flag.
+      env:
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
       run: |
         cd /opt/monai
         nvidia-smi
@@ -221,7 +237,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     needs: cron-gpu  # so that monai itself is verified first
     container:
-      image: nvcr.io/nvidia/pytorch:23.08-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:24.10-py3  # testing with the latest pytorch base image
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, integration]
     steps:

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -100,3 +100,6 @@ jobs:
       shell: bash
       env:
         QUICKTEST: True
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
diff --git a/.github/workflows/integration.yml b/.github/workflows/integration.yml
@@ -68,6 +68,9 @@ jobs:
       shell: bash
       env:
         BUILD_MONAI: 1
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
       run: ./runtests.sh --build --net
 
     - name: Add reaction

diff --git a/.github/workflows/pythonapp-gpu.yml b/.github/workflows/pythonapp-gpu.yml
@@ -29,10 +29,6 @@ jobs:
           - "PT210+CUDA121DOCKER"
         include:
           # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
-          - environment: PT19+CUDA114DOCKER
-            # 21.10: 1.10.0a0+0aef44c
-            pytorch: "-h"  # we explicitly set pytorch to -h to avoid pip install error
-            base: "nvcr.io/nvidia/pytorch:21.10-py3"
           - environment: PT110+CUDA111
             pytorch: "torch==1.10.2 torchvision==0.11.3 --extra-index-url https://download.pytorch.org/whl/cu111"
             base: "nvcr.io/nvidia/cuda:11.1.1-devel-ubuntu18.04"
@@ -47,6 +43,10 @@ jobs:
             # 23.08: 2.1.0a0+29c30b1
             pytorch: "-h"  # we explicitly set pytorch to -h to avoid pip install error
             base: "nvcr.io/nvidia/pytorch:23.08-py3"
+          - environment: PT210+CUDA121DOCKER
+            # 24.08: 2.3.0a0+40ec155e58.nv24.3
+            pytorch: "-h"  # we explicitly set pytorch to -h to avoid pip install error
+            base: "nvcr.io/nvidia/pytorch:24.08-py3"
     container:
       image: ${{ matrix.base }}
       options: --gpus all --env NVIDIA_DISABLE_REQUIRE=true  # workaround for unsatisfied condition: cuda>=11.6
@@ -62,7 +62,7 @@ jobs:
         if [ ${{ matrix.environment }} = "PT110+CUDA111" ] || \
           [ ${{ matrix.environment }} = "PT113+CUDA116" ]
         then
-        PYVER=3.8 PYSFX=3 DISTUTILS=python3-distutils && \
+        PYVER=3.9 PYSFX=3 DISTUTILS=python3-distutils && \
         apt-get update && apt-get install -y --no-install-recommends \
           curl \
           pkg-config \

diff --git a/.github/workflows/pythonapp-min.yml b/.github/workflows/pythonapp-min.yml
@@ -9,6 +9,8 @@ on:
       - main
       - releasing/*
   pull_request:
+    head_ref-ignore:
+      - dev
 
 concurrency:
   # automatically cancel the previously triggered workflows when there's a newer version
@@ -29,10 +31,10 @@ jobs:
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: Prepare pip wheel
       run: |
         which python
@@ -65,13 +67,16 @@ jobs:
       shell: bash
       env:
         QUICKTEST: True
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
 
   min-dep-py3:  # min dependencies installed tests for different python
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v4
@@ -110,20 +115,23 @@ jobs:
         ./runtests.sh --min
       env:
         QUICKTEST: True
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
 
   min-dep-pytorch:  # min dependencies installed tests for different pytorch
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        pytorch-version: ['1.9.1', '1.10.2', '1.11.0', '1.12.1', '1.13', 'latest']
+        pytorch-version: ['1.10.2', '1.11.0', '1.12.1', '1.13', '2.0.1', 'latest']
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: Prepare pip wheel
       run: |
         which python
@@ -159,3 +167,6 @@ jobs:
         ./runtests.sh --min
       env:
         QUICKTEST: True
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
@@ -9,6 +9,8 @@ on:
       - main
       - releasing/*
   pull_request:
+    head_ref-ignore:
+      - dev
 
 concurrency:
   # automatically cancel the previously triggered workflows when there's a newer version
@@ -27,10 +29,10 @@ jobs:
         opt: ["codeformat", "pytype", "mypy"]
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: cache weekly timestamp
       id: pip-cache
       run: |
@@ -43,6 +45,7 @@ jobs:
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install dependencies
       run: |
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --upgrade pip wheel
         python -m pip install -r requirements-dev.txt
     - name: Lint and type check
@@ -68,10 +71,10 @@ jobs:
         maximum-size: 16GB
         disk-root: "D:"
     - uses: actions/checkout@v4
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: Prepare pip wheel
       run: |
         which python
@@ -96,8 +99,10 @@ jobs:
       name: Install itk pre-release (Linux only)
       run: |
         python -m pip install --pre -U itk
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
     - name: Install the dependencies
       run: |
+        python -m pip install --user --upgrade pip wheel
         python -m pip install torch==1.13.1 torchvision==0.14.1
         cat "requirements-dev.txt"
         python -m pip install -r requirements-dev.txt
@@ -127,10 +132,10 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: cache weekly timestamp
       id: pip-cache
       run: |
@@ -145,7 +150,8 @@ jobs:
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install dependencies
       run: |
-        python -m pip install --user --upgrade pip setuptools wheel twine
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
+        python -m pip install --user --upgrade pip setuptools wheel twine packaging
         # install the latest pytorch for testing
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
         # fresh torch installation according to pyproject.toml
@@ -208,10 +214,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: cache weekly timestamp
       id: pip-cache
       run: |